Starting phenix.real_space_refine on Mon Aug 25 19:38:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zk2_60165/08_2025/8zk2_60165.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zk2_60165/08_2025/8zk2_60165.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zk2_60165/08_2025/8zk2_60165.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zk2_60165/08_2025/8zk2_60165.map" model { file = "/net/cci-nas-00/data/ceres_data/8zk2_60165/08_2025/8zk2_60165.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zk2_60165/08_2025/8zk2_60165.cif" } resolution = 2.65 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.065 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4470 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 5 7.16 5 P 7 5.49 5 Mg 55 5.21 5 S 133 5.16 5 C 18777 2.51 5 N 3834 2.21 5 O 4137 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26948 Number of models: 1 Model: "" Number of chains: 72 Chain: "C" Number of atoms: 2618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2618 Classifications: {'peptide': 342} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 314} Chain: "L" Number of atoms: 2163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2163 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 15, 'TRANS': 257} Chain: "M" Number of atoms: 2269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2269 Classifications: {'peptide': 287} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 269} Chain: "H" Number of atoms: 1906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1906 Classifications: {'peptide': 245} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 224} Chain breaks: 1 Chain: "B" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 377 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "A" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 424 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "D" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 377 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "E" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 424 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "F" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 377 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "G" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 424 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "I" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 377 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "J" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 424 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "K" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 377 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "N" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 424 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "O" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 377 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "P" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 424 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "Q" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 377 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "R" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 424 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "S" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 377 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "T" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 424 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "U" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 377 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "V" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 424 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "W" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 377 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "X" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 424 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "Y" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 377 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "Z" Number of atoms: 369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 369 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "a" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 377 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "b" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 424 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "c" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 377 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "d" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 424 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "e" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 377 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "f" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 424 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "g" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 377 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "h" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 424 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "i" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 377 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "j" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 424 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "C" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 229 Unusual residues: {' MG': 3, '8K6': 1, 'HEC': 4, 'PGV': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Chain: "L" Number of atoms: 338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 338 Unusual residues: {'8K6': 5, 'BCL': 2, 'BPH': 1, 'LMT': 1, 'PGV': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 4 Chain: "M" Number of atoms: 401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 401 Unusual residues: {' FE': 1, '8K6': 1, 'BCL': 2, 'BPH': 1, 'CRT': 1, 'MQ8': 1, 'PGV': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 171 Unusual residues: {' MG': 1, '8K6': 4, 'PGV': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 110 Unusual residues: {'BCL': 1, 'CRT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 176 Unusual residues: {'BCL': 2, 'CRT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 176 Unusual residues: {'BCL': 2, 'CRT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 110 Unusual residues: {'BCL': 1, 'CRT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 163 Unusual residues: {'8K6': 2, 'BCL': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "K" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 110 Unusual residues: {'BCL': 1, 'CRT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 194 Unusual residues: {'8K6': 1, 'BCL': 2, 'CRT': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "O" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 194 Unusual residues: {'8K6': 1, 'BCL': 2, 'CRT': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "Q" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 227 Unusual residues: {'BCL': 2, 'CRT': 1, 'PGV': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "S" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "U" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 110 Unusual residues: {'BCL': 1, 'CRT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 168 Unusual residues: {'8K6': 2, 'BCL': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "W" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 110 Unusual residues: {'BCL': 1, 'CRT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'8K6': 1, 'BCL': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Y" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 110 Unusual residues: {'BCL': 1, 'CRT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Z" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 152 Unusual residues: {'BCL': 1, 'CRT': 1, 'PGV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "a" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 110 Unusual residues: {'BCL': 1, 'CRT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "b" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "c" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "d" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'8K6': 1, 'BCL': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "e" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 110 Unusual residues: {'BCL': 1, 'CRT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "f" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'8K6': 1, 'BCL': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "g" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "h" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "i" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 110 Unusual residues: {'BCL': 1, 'CRT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "j" Number of atoms: 212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 212 Unusual residues: {'8K6': 2, 'BCL': 2, 'CRT': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 5.24, per 1000 atoms: 0.19 Number of scatterers: 26948 At special positions: 0 Unit cell: (139.36, 126.88, 133.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 5 26.01 S 133 16.00 P 7 15.00 Mg 55 11.99 O 4137 8.00 N 3834 7.00 C 18777 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=63, symmetry=0 Number of additional bonds: simple=63, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.26 Conformation dependent library (CDL) restraints added in 992.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 5396 Ramachandran restraints generated. 2698 Oldfield, 0 Emsley, 2698 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5122 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 9 sheets defined 62.1% alpha, 2.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'C' and resid 26 through 45 Processing helix chain 'C' and resid 66 through 75 Processing helix chain 'C' and resid 76 through 80 Processing helix chain 'C' and resid 94 through 99 removed outlier: 3.538A pdb=" N VAL C 98 " --> pdb=" O LEU C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 124 Processing helix chain 'C' and resid 128 through 133 removed outlier: 3.888A pdb=" N ASN C 131 " --> pdb=" O GLU C 128 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N CYS C 133 " --> pdb=" O CYS C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 164 removed outlier: 3.823A pdb=" N ILE C 148 " --> pdb=" O PRO C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 169 Processing helix chain 'C' and resid 174 through 179 removed outlier: 4.301A pdb=" N CYS C 178 " --> pdb=" O THR C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 216 Processing helix chain 'C' and resid 224 through 229 Processing helix chain 'C' and resid 252 through 271 Processing helix chain 'C' and resid 273 through 277 Processing helix chain 'C' and resid 291 through 310 removed outlier: 3.581A pdb=" N THR C 295 " --> pdb=" O PRO C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 318 Processing helix chain 'C' and resid 333 through 339 removed outlier: 4.113A pdb=" N CYS C 337 " --> pdb=" O ASN C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 348 removed outlier: 3.542A pdb=" N GLU C 348 " --> pdb=" O MET C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 359 removed outlier: 3.997A pdb=" N ALA C 359 " --> pdb=" O SER C 356 " (cutoff:3.500A) Processing helix chain 'L' and resid 7 through 11 Processing helix chain 'L' and resid 33 through 56 Processing helix chain 'L' and resid 72 through 76 Processing helix chain 'L' and resid 85 through 114 Processing helix chain 'L' and resid 117 through 135 removed outlier: 3.617A pdb=" N PHE L 125 " --> pdb=" O PHE L 121 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA L 126 " --> pdb=" O ALA L 122 " (cutoff:3.500A) Processing helix chain 'L' and resid 135 through 142 Processing helix chain 'L' and resid 143 through 147 Processing helix chain 'L' and resid 153 through 165 removed outlier: 3.506A pdb=" N ASP L 157 " --> pdb=" O MET L 153 " (cutoff:3.500A) Processing helix chain 'L' and resid 166 through 167 No H-bonds generated for 'chain 'L' and resid 166 through 167' Processing helix chain 'L' and resid 168 through 171 Processing helix chain 'L' and resid 172 through 201 Processing helix chain 'L' and resid 210 through 222 removed outlier: 3.657A pdb=" N PHE L 218 " --> pdb=" O GLU L 214 " (cutoff:3.500A) Processing helix chain 'L' and resid 227 through 252 removed outlier: 3.509A pdb=" N ILE L 231 " --> pdb=" O GLY L 227 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N HIS L 232 " --> pdb=" O THR L 228 " (cutoff:3.500A) Processing helix chain 'L' and resid 261 through 264 Processing helix chain 'L' and resid 265 through 270 Processing helix chain 'M' and resid 39 through 44 removed outlier: 3.832A pdb=" N ILE M 43 " --> pdb=" O TRP M 39 " (cutoff:3.500A) Processing helix chain 'M' and resid 53 through 78 Processing helix chain 'M' and resid 82 through 90 Processing helix chain 'M' and resid 99 through 103 Processing helix chain 'M' and resid 109 through 112 Processing helix chain 'M' and resid 113 through 141 Processing helix chain 'M' and resid 145 through 163 removed outlier: 3.640A pdb=" N TRP M 149 " --> pdb=" O THR M 145 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER M 153 " --> pdb=" O TRP M 149 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA M 154 " --> pdb=" O ALA M 150 " (cutoff:3.500A) Processing helix chain 'M' and resid 163 through 170 Processing helix chain 'M' and resid 171 through 175 Processing helix chain 'M' and resid 180 through 194 removed outlier: 3.806A pdb=" N LEU M 184 " --> pdb=" O ILE M 180 " (cutoff:3.500A) Processing helix chain 'M' and resid 196 through 199 Processing helix chain 'M' and resid 200 through 227 Processing helix chain 'M' and resid 228 through 231 Processing helix chain 'M' and resid 234 through 241 Processing helix chain 'M' and resid 243 through 258 removed outlier: 3.614A pdb=" N TRP M 253 " --> pdb=" O ALA M 249 " (cutoff:3.500A) Processing helix chain 'M' and resid 264 through 287 removed outlier: 3.937A pdb=" N THR M 278 " --> pdb=" O ALA M 274 " (cutoff:3.500A) Processing helix chain 'M' and resid 294 through 302 Processing helix chain 'H' and resid 10 through 34 Processing helix chain 'H' and resid 101 through 106 Processing helix chain 'H' and resid 107 through 111 Processing helix chain 'H' and resid 200 through 202 No H-bonds generated for 'chain 'H' and resid 200 through 202' Processing helix chain 'H' and resid 217 through 222 removed outlier: 3.552A pdb=" N ALA H 222 " --> pdb=" O ALA H 218 " (cutoff:3.500A) Processing helix chain 'H' and resid 234 through 252 removed outlier: 3.809A pdb=" N THR H 249 " --> pdb=" O TYR H 245 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LEU H 250 " --> pdb=" O ALA H 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 47 removed outlier: 3.663A pdb=" N VAL B 24 " --> pdb=" O GLU B 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 5 through 11 removed outlier: 3.959A pdb=" N TRP A 9 " --> pdb=" O HIS A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 13 through 38 Processing helix chain 'D' and resid 14 through 47 Processing helix chain 'E' and resid 5 through 11 removed outlier: 3.875A pdb=" N TRP E 9 " --> pdb=" O HIS E 6 " (cutoff:3.500A) Processing helix chain 'E' and resid 13 through 38 Processing helix chain 'F' and resid 14 through 47 removed outlier: 3.569A pdb=" N LYS F 19 " --> pdb=" O GLU F 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 11 removed outlier: 3.750A pdb=" N TRP G 9 " --> pdb=" O HIS G 6 " (cutoff:3.500A) Processing helix chain 'G' and resid 13 through 38 Processing helix chain 'I' and resid 14 through 47 Processing helix chain 'J' and resid 5 through 11 removed outlier: 3.752A pdb=" N TRP J 9 " --> pdb=" O HIS J 6 " (cutoff:3.500A) Processing helix chain 'J' and resid 13 through 38 Processing helix chain 'K' and resid 14 through 47 Processing helix chain 'N' and resid 5 through 11 removed outlier: 3.766A pdb=" N VAL N 8 " --> pdb=" O THR N 5 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N TRP N 9 " --> pdb=" O HIS N 6 " (cutoff:3.500A) Processing helix chain 'N' and resid 13 through 38 Processing helix chain 'O' and resid 16 through 47 removed outlier: 3.562A pdb=" N VAL O 24 " --> pdb=" O GLU O 20 " (cutoff:3.500A) Processing helix chain 'P' and resid 5 through 11 removed outlier: 3.786A pdb=" N TRP P 9 " --> pdb=" O HIS P 6 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU P 10 " --> pdb=" O LYS P 7 " (cutoff:3.500A) Processing helix chain 'P' and resid 13 through 38 Processing helix chain 'Q' and resid 14 through 47 Processing helix chain 'R' and resid 5 through 11 removed outlier: 3.777A pdb=" N VAL R 8 " --> pdb=" O THR R 5 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N TRP R 9 " --> pdb=" O HIS R 6 " (cutoff:3.500A) Processing helix chain 'R' and resid 13 through 38 Processing helix chain 'S' and resid 14 through 47 Processing helix chain 'T' and resid 5 through 11 removed outlier: 3.583A pdb=" N VAL T 8 " --> pdb=" O THR T 5 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N TRP T 9 " --> pdb=" O HIS T 6 " (cutoff:3.500A) Processing helix chain 'T' and resid 13 through 38 Processing helix chain 'U' and resid 14 through 47 Processing helix chain 'V' and resid 5 through 11 removed outlier: 3.830A pdb=" N VAL V 8 " --> pdb=" O THR V 5 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TRP V 9 " --> pdb=" O HIS V 6 " (cutoff:3.500A) Processing helix chain 'V' and resid 13 through 38 Processing helix chain 'W' and resid 14 through 47 Processing helix chain 'X' and resid 5 through 11 removed outlier: 3.536A pdb=" N VAL X 8 " --> pdb=" O THR X 5 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N TRP X 9 " --> pdb=" O HIS X 6 " (cutoff:3.500A) Processing helix chain 'X' and resid 13 through 38 Processing helix chain 'Y' and resid 14 through 47 Processing helix chain 'Z' and resid 6 through 11 removed outlier: 4.406A pdb=" N TRP Z 9 " --> pdb=" O HIS Z 6 " (cutoff:3.500A) Processing helix chain 'Z' and resid 13 through 38 Processing helix chain 'a' and resid 14 through 47 Processing helix chain 'b' and resid 5 through 11 removed outlier: 3.662A pdb=" N VAL b 8 " --> pdb=" O THR b 5 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TRP b 9 " --> pdb=" O HIS b 6 " (cutoff:3.500A) Processing helix chain 'b' and resid 13 through 38 Processing helix chain 'c' and resid 14 through 47 Processing helix chain 'd' and resid 5 through 11 removed outlier: 3.564A pdb=" N VAL d 8 " --> pdb=" O THR d 5 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N TRP d 9 " --> pdb=" O HIS d 6 " (cutoff:3.500A) Processing helix chain 'd' and resid 13 through 38 removed outlier: 4.882A pdb=" N VAL d 19 " --> pdb=" O ARG d 15 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N ALA d 20 " --> pdb=" O SER d 16 " (cutoff:3.500A) Processing helix chain 'e' and resid 16 through 47 Processing helix chain 'f' and resid 5 through 11 removed outlier: 3.997A pdb=" N VAL f 8 " --> pdb=" O THR f 5 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TRP f 9 " --> pdb=" O HIS f 6 " (cutoff:3.500A) Processing helix chain 'f' and resid 13 through 38 removed outlier: 3.565A pdb=" N LEU f 18 " --> pdb=" O PRO f 14 " (cutoff:3.500A) Processing helix chain 'g' and resid 14 through 47 removed outlier: 3.654A pdb=" N VAL g 24 " --> pdb=" O GLU g 20 " (cutoff:3.500A) Processing helix chain 'h' and resid 5 through 11 removed outlier: 3.655A pdb=" N VAL h 8 " --> pdb=" O THR h 5 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TRP h 9 " --> pdb=" O HIS h 6 " (cutoff:3.500A) Processing helix chain 'h' and resid 13 through 39 Processing helix chain 'i' and resid 14 through 47 Processing helix chain 'j' and resid 5 through 11 removed outlier: 3.550A pdb=" N VAL j 8 " --> pdb=" O THR j 5 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TRP j 9 " --> pdb=" O HIS j 6 " (cutoff:3.500A) Processing helix chain 'j' and resid 13 through 38 Processing sheet with id=AA1, first strand: chain 'C' and resid 50 through 53 Processing sheet with id=AA2, first strand: chain 'C' and resid 188 through 189 Processing sheet with id=AA3, first strand: chain 'L' and resid 25 through 27 removed outlier: 3.643A pdb=" N PHE L 25 " --> pdb=" O VAL L 32 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'M' and resid 35 through 36 removed outlier: 3.687A pdb=" N THR M 35 " --> pdb=" O ILE M 48 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'M' and resid 94 through 95 Processing sheet with id=AA6, first strand: chain 'H' and resid 61 through 64 Processing sheet with id=AA7, first strand: chain 'H' and resid 85 through 86 Processing sheet with id=AA8, first strand: chain 'H' and resid 129 through 131 removed outlier: 6.386A pdb=" N GLY H 161 " --> pdb=" O LEU H 182 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LEU H 182 " --> pdb=" O GLY H 161 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL H 163 " --> pdb=" O VAL H 180 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL H 180 " --> pdb=" O VAL H 163 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ASP H 165 " --> pdb=" O LEU H 178 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N LEU H 178 " --> pdb=" O ASP H 165 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N TRP H 167 " --> pdb=" O ARG H 176 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE H 174 " --> pdb=" O ASP H 169 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 129 through 131 removed outlier: 6.638A pdb=" N THR H 159 " --> pdb=" O ALA H 154 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ALA H 154 " --> pdb=" O THR H 159 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY H 161 " --> pdb=" O VAL H 152 " (cutoff:3.500A) 1319 hydrogen bonds defined for protein. 3735 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.07 Time building geometry restraints manager: 3.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.38: 8759 1.38 - 1.58: 18873 1.58 - 1.79: 88 1.79 - 2.00: 176 2.00 - 2.20: 191 Bond restraints: 28087 Sorted by residual: bond pdb=" NA BCL M 403 " pdb="MG BCL M 403 " ideal model delta sigma weight residual 2.170 1.977 0.193 2.40e-02 1.74e+03 6.45e+01 bond pdb=" NA BCL G 101 " pdb="MG BCL G 101 " ideal model delta sigma weight residual 2.170 1.983 0.187 2.40e-02 1.74e+03 6.09e+01 bond pdb=" NA BCL P 101 " pdb="MG BCL P 101 " ideal model delta sigma weight residual 2.170 1.983 0.187 2.40e-02 1.74e+03 6.05e+01 bond pdb=" NA BCL M 402 " pdb="MG BCL M 402 " ideal model delta sigma weight residual 2.170 1.984 0.186 2.40e-02 1.74e+03 6.02e+01 bond pdb=" NA BCL f 101 " pdb="MG BCL f 101 " ideal model delta sigma weight residual 2.170 1.985 0.185 2.40e-02 1.74e+03 5.96e+01 ... (remaining 28082 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.73: 38046 6.73 - 13.46: 722 13.46 - 20.19: 52 20.19 - 26.92: 2 26.92 - 33.65: 2 Bond angle restraints: 38824 Sorted by residual: angle pdb=" ND BCL M 403 " pdb="MG BCL M 403 " pdb=" NA BCL M 403 " ideal model delta sigma weight residual 88.02 97.69 -9.66 1.29e+00 6.02e-01 5.62e+01 angle pdb=" C1D BCL d 102 " pdb=" C2D BCL d 102 " pdb=" CMD BCL d 102 " ideal model delta sigma weight residual 125.57 139.08 -13.50 1.83e+00 2.99e-01 5.46e+01 angle pdb=" ND BCL J 101 " pdb="MG BCL J 101 " pdb=" NA BCL J 101 " ideal model delta sigma weight residual 88.02 97.51 -9.48 1.29e+00 6.02e-01 5.41e+01 angle pdb=" ND BCL f 101 " pdb="MG BCL f 101 " pdb=" NA BCL f 101 " ideal model delta sigma weight residual 88.02 97.37 -9.35 1.29e+00 6.02e-01 5.26e+01 angle pdb=" ND BCL h 101 " pdb="MG BCL h 101 " pdb=" NA BCL h 101 " ideal model delta sigma weight residual 88.02 97.30 -9.27 1.29e+00 6.02e-01 5.18e+01 ... (remaining 38819 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.82: 14210 35.82 - 71.63: 639 71.63 - 107.45: 62 107.45 - 143.26: 15 143.26 - 179.08: 10 Dihedral angle restraints: 14936 sinusoidal: 7021 harmonic: 7915 Sorted by residual: dihedral pdb=" C1 BCL h 102 " pdb=" CGA BCL h 102 " pdb=" O2A BCL h 102 " pdb=" CBA BCL h 102 " ideal model delta sinusoidal sigma weight residual -180.00 -0.92 -179.08 1 6.00e+00 2.78e-02 5.33e+02 dihedral pdb=" C1 BCL X 102 " pdb=" CGA BCL X 102 " pdb=" O2A BCL X 102 " pdb=" CBA BCL X 102 " ideal model delta sinusoidal sigma weight residual -180.00 -1.96 -178.04 1 6.00e+00 2.78e-02 5.33e+02 dihedral pdb=" C1 BCL V 102 " pdb=" CGA BCL V 102 " pdb=" O2A BCL V 102 " pdb=" CBA BCL V 102 " ideal model delta sinusoidal sigma weight residual 180.00 2.41 177.59 1 6.00e+00 2.78e-02 5.33e+02 ... (remaining 14933 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 3215 0.066 - 0.132: 431 0.132 - 0.198: 104 0.198 - 0.263: 19 0.263 - 0.329: 11 Chirality restraints: 3780 Sorted by residual: chirality pdb=" CBD BCL I 101 " pdb=" CAD BCL I 101 " pdb=" CGD BCL I 101 " pdb=" CHA BCL I 101 " both_signs ideal model delta sigma weight residual False 2.62 2.29 0.33 2.00e-01 2.50e+01 2.71e+00 chirality pdb=" CBD BCL B 101 " pdb=" CAD BCL B 101 " pdb=" CGD BCL B 101 " pdb=" CHA BCL B 101 " both_signs ideal model delta sigma weight residual False 2.62 2.30 0.32 2.00e-01 2.50e+01 2.53e+00 chirality pdb=" CA VAL W 57 " pdb=" N VAL W 57 " pdb=" C VAL W 57 " pdb=" CB VAL W 57 " both_signs ideal model delta sigma weight residual False 2.44 2.74 -0.30 2.00e-01 2.50e+01 2.26e+00 ... (remaining 3777 not shown) Planarity restraints: 4704 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 BCL G 102 " -0.350 3.00e-02 1.11e+03 2.87e-01 4.58e+02 pdb=" CBA BCL G 102 " -0.176 3.00e-02 1.11e+03 pdb=" CGA BCL G 102 " 0.081 3.00e-02 1.11e+03 pdb=" O1A BCL G 102 " -0.054 3.00e-02 1.11e+03 pdb=" O2A BCL G 102 " 0.499 3.00e-02 1.11e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BCL J 102 " -0.352 3.00e-02 1.11e+03 2.86e-01 4.55e+02 pdb=" CBA BCL J 102 " -0.190 3.00e-02 1.11e+03 pdb=" CGA BCL J 102 " 0.086 3.00e-02 1.11e+03 pdb=" O1A BCL J 102 " -0.034 3.00e-02 1.11e+03 pdb=" O2A BCL J 102 " 0.491 3.00e-02 1.11e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BCL M 402 " -0.327 3.00e-02 1.11e+03 2.71e-01 4.07e+02 pdb=" CBA BCL M 402 " -0.152 3.00e-02 1.11e+03 pdb=" CGA BCL M 402 " 0.064 3.00e-02 1.11e+03 pdb=" O1A BCL M 402 " -0.063 3.00e-02 1.11e+03 pdb=" O2A BCL M 402 " 0.478 3.00e-02 1.11e+03 ... (remaining 4701 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 259 2.62 - 3.19: 20984 3.19 - 3.76: 45735 3.76 - 4.33: 69564 4.33 - 4.90: 110746 Nonbonded interactions: 247288 Sorted by model distance: nonbonded pdb=" NE2 HIS C 338 " pdb="FE HEC C 504 " model vdw 2.047 3.080 nonbonded pdb=" OD2 ASP C 214 " pdb="MG MG C 506 " model vdw 2.070 2.170 nonbonded pdb=" OD1 ASP C 194 " pdb="MG MG C 506 " model vdw 2.073 2.170 nonbonded pdb=" NE2 HIS L 192 " pdb="FE FE M 401 " model vdw 2.144 2.340 nonbonded pdb=" NE2 HIS M 220 " pdb="FE FE M 401 " model vdw 2.147 2.340 ... (remaining 247283 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 6 through 51) selection = (chain 'E' and resid 6 through 51) selection = (chain 'G' and resid 6 through 51) selection = (chain 'J' and resid 6 through 51) selection = (chain 'N' and resid 6 through 51) selection = (chain 'P' and resid 6 through 51) selection = (chain 'R' and resid 6 through 51) selection = (chain 'T' and resid 6 through 51) selection = (chain 'V' and resid 6 through 51) selection = (chain 'X' and resid 6 through 51) selection = (chain 'Z' and resid 6 through 51) selection = (chain 'b' and resid 6 through 51) selection = (chain 'd' and resid 6 through 51) selection = (chain 'f' and resid 6 through 51) selection = (chain 'h' and resid 6 through 51) selection = (chain 'j' and resid 6 through 51) } ncs_group { reference = (chain 'B' and resid 9 through 101) selection = chain 'D' selection = chain 'F' selection = (chain 'I' and resid 9 through 101) selection = (chain 'K' and resid 9 through 101) selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = (chain 'U' and resid 9 through 101) selection = (chain 'W' and resid 9 through 101) selection = (chain 'Y' and resid 9 through 101) selection = (chain 'a' and resid 9 through 101) selection = chain 'c' selection = (chain 'e' and resid 9 through 101) selection = chain 'g' selection = (chain 'i' and resid 9 through 101) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.050 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 21.430 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.022 0.348 28150 Z= 1.025 Angle : 2.009 33.654 38824 Z= 0.905 Chirality : 0.055 0.329 3780 Planarity : 0.021 0.287 4704 Dihedral : 19.507 179.077 9814 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.05 % Allowed : 0.41 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.75 (0.16), residues: 2698 helix: 2.14 (0.13), residues: 1492 sheet: 0.58 (0.98), residues: 26 loop : -0.05 (0.18), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 57 TYR 0.021 0.002 TYR M 194 PHE 0.058 0.002 PHE L 218 TRP 0.014 0.001 TRP U 50 HIS 0.016 0.001 HIS M 183 Details of bonding type rmsd covalent geometry : bond 0.02085 (28087) covalent geometry : angle 2.00870 (38824) hydrogen bonds : bond 0.12040 ( 1317) hydrogen bonds : angle 4.73226 ( 3735) Misc. bond : bond 0.11981 ( 63) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5396 Ramachandran restraints generated. 2698 Oldfield, 0 Emsley, 2698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5396 Ramachandran restraints generated. 2698 Oldfield, 0 Emsley, 2698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 310 time to evaluate : 0.672 Fit side-chains REVERT: H 1 MET cc_start: 0.7285 (mmt) cc_final: 0.6864 (mpt) REVERT: E 1 MET cc_start: 0.7695 (ttm) cc_final: 0.7183 (mtp) REVERT: F 27 GLN cc_start: 0.8063 (mt0) cc_final: 0.7854 (mt0) REVERT: U 27 GLN cc_start: 0.7945 (mt0) cc_final: 0.7634 (mt0) REVERT: V 46 GLU cc_start: 0.8138 (tp30) cc_final: 0.7934 (mm-30) outliers start: 1 outliers final: 0 residues processed: 311 average time/residue: 0.6387 time to fit residues: 227.1468 Evaluate side-chains 273 residues out of total 2194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 273 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.1980 chunk 132 optimal weight: 0.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 146 HIS L 168 HIS H 90 ASN ** H 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 253 ASN T 39 HIS W 27 GLN i 27 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.114938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.097172 restraints weight = 31378.554| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 1.17 r_work: 0.2959 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.0889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.398 28150 Z= 0.155 Angle : 0.813 13.480 38824 Z= 0.301 Chirality : 0.037 0.173 3780 Planarity : 0.005 0.069 4704 Dihedral : 19.232 179.476 5265 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.73 % Allowed : 6.47 % Favored : 92.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.93 (0.16), residues: 2698 helix: 2.30 (0.12), residues: 1495 sheet: 0.60 (1.03), residues: 26 loop : -0.01 (0.18), residues: 1177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG j 15 TYR 0.023 0.002 TYR M 194 PHE 0.035 0.002 PHE L 218 TRP 0.012 0.001 TRP A 9 HIS 0.009 0.001 HIS M 183 Details of bonding type rmsd covalent geometry : bond 0.00376 (28087) covalent geometry : angle 0.81268 (38824) hydrogen bonds : bond 0.04374 ( 1317) hydrogen bonds : angle 3.99363 ( 3735) Misc. bond : bond 0.13252 ( 63) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5396 Ramachandran restraints generated. 2698 Oldfield, 0 Emsley, 2698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5396 Ramachandran restraints generated. 2698 Oldfield, 0 Emsley, 2698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 290 time to evaluate : 1.141 Fit side-chains REVERT: C 214 ASP cc_start: 0.8644 (m-30) cc_final: 0.8242 (m-30) REVERT: M 80 ASP cc_start: 0.8027 (m-30) cc_final: 0.7693 (m-30) REVERT: E 1 MET cc_start: 0.7182 (ttm) cc_final: 0.6888 (mtp) REVERT: F 27 GLN cc_start: 0.8448 (mt0) cc_final: 0.8222 (mt0) REVERT: F 54 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7501 (pp20) REVERT: U 27 GLN cc_start: 0.8203 (mt0) cc_final: 0.7900 (mt0) REVERT: f 11 MET cc_start: 0.8484 (OUTLIER) cc_final: 0.8084 (ttm) REVERT: i 19 LYS cc_start: 0.7959 (tttt) cc_final: 0.7685 (tttm) outliers start: 16 outliers final: 4 residues processed: 298 average time/residue: 0.6320 time to fit residues: 216.9901 Evaluate side-chains 269 residues out of total 2194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 263 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 259 LYS Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain F residue 54 GLU Chi-restraints excluded: chain b residue 16 SER Chi-restraints excluded: chain f residue 11 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 21 optimal weight: 6.9990 chunk 47 optimal weight: 0.9980 chunk 124 optimal weight: 0.8980 chunk 251 optimal weight: 30.0000 chunk 52 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 243 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 244 optimal weight: 0.6980 chunk 146 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 168 HIS H 90 ASN W 27 GLN i 27 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.112598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.095445 restraints weight = 31624.597| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 1.09 r_work: 0.2925 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.1240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.379 28150 Z= 0.185 Angle : 0.784 14.663 38824 Z= 0.304 Chirality : 0.039 0.149 3780 Planarity : 0.005 0.062 4704 Dihedral : 19.040 179.876 5265 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.46 % Allowed : 7.61 % Favored : 90.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.90 (0.15), residues: 2698 helix: 2.27 (0.12), residues: 1495 sheet: 0.52 (1.05), residues: 26 loop : -0.01 (0.18), residues: 1177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG d 15 TYR 0.025 0.002 TYR M 194 PHE 0.028 0.002 PHE L 218 TRP 0.012 0.001 TRP f 9 HIS 0.008 0.001 HIS M 183 Details of bonding type rmsd covalent geometry : bond 0.00451 (28087) covalent geometry : angle 0.78434 (38824) hydrogen bonds : bond 0.04447 ( 1317) hydrogen bonds : angle 3.94244 ( 3735) Misc. bond : bond 0.11993 ( 63) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5396 Ramachandran restraints generated. 2698 Oldfield, 0 Emsley, 2698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5396 Ramachandran restraints generated. 2698 Oldfield, 0 Emsley, 2698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 285 time to evaluate : 0.803 Fit side-chains revert: symmetry clash REVERT: C 57 ARG cc_start: 0.8765 (OUTLIER) cc_final: 0.7454 (ptm-80) REVERT: L 79 PHE cc_start: 0.8464 (m-80) cc_final: 0.8104 (m-80) REVERT: L 226 ILE cc_start: 0.7863 (tp) cc_final: 0.7662 (tt) REVERT: M 80 ASP cc_start: 0.8112 (m-30) cc_final: 0.7800 (m-30) REVERT: H 121 LYS cc_start: 0.8541 (mmtm) cc_final: 0.8185 (mmtp) REVERT: E 1 MET cc_start: 0.7514 (ttm) cc_final: 0.7010 (mtp) REVERT: U 27 GLN cc_start: 0.8318 (mt0) cc_final: 0.8061 (mt0) REVERT: V 15 ARG cc_start: 0.8249 (OUTLIER) cc_final: 0.7207 (ttp-110) REVERT: c 15 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.6570 (tm-30) REVERT: f 11 MET cc_start: 0.8505 (OUTLIER) cc_final: 0.8074 (ttm) REVERT: i 19 LYS cc_start: 0.8142 (tttt) cc_final: 0.7888 (tttm) outliers start: 32 outliers final: 13 residues processed: 299 average time/residue: 0.6577 time to fit residues: 225.9815 Evaluate side-chains 291 residues out of total 2194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 274 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 57 ARG Chi-restraints excluded: chain C residue 264 PHE Chi-restraints excluded: chain L residue 259 LYS Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 307 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain F residue 54 GLU Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain N residue 52 THR Chi-restraints excluded: chain P residue 35 LEU Chi-restraints excluded: chain P residue 52 THR Chi-restraints excluded: chain V residue 15 ARG Chi-restraints excluded: chain W residue 13 LEU Chi-restraints excluded: chain b residue 16 SER Chi-restraints excluded: chain c residue 15 GLU Chi-restraints excluded: chain f residue 11 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 165 optimal weight: 3.9990 chunk 247 optimal weight: 0.0570 chunk 60 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 176 optimal weight: 7.9990 chunk 20 optimal weight: 0.0010 chunk 114 optimal weight: 0.9990 chunk 7 optimal weight: 9.9990 chunk 62 optimal weight: 7.9990 chunk 1 optimal weight: 3.9990 chunk 215 optimal weight: 1.9990 overall best weight: 1.0110 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 168 HIS H 90 ASN W 27 GLN i 27 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.113458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.096024 restraints weight = 31403.118| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 1.17 r_work: 0.2937 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.344 28150 Z= 0.153 Angle : 0.736 11.658 38824 Z= 0.284 Chirality : 0.037 0.140 3780 Planarity : 0.005 0.058 4704 Dihedral : 18.740 179.938 5265 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.55 % Allowed : 8.93 % Favored : 89.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.08 (0.15), residues: 2698 helix: 2.42 (0.12), residues: 1495 sheet: 0.63 (1.08), residues: 26 loop : 0.07 (0.18), residues: 1177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 13 TYR 0.023 0.002 TYR M 194 PHE 0.028 0.002 PHE L 218 TRP 0.013 0.001 TRP L 265 HIS 0.008 0.001 HIS M 183 Details of bonding type rmsd covalent geometry : bond 0.00368 (28087) covalent geometry : angle 0.73554 (38824) hydrogen bonds : bond 0.04214 ( 1317) hydrogen bonds : angle 3.84166 ( 3735) Misc. bond : bond 0.11843 ( 63) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5396 Ramachandran restraints generated. 2698 Oldfield, 0 Emsley, 2698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5396 Ramachandran restraints generated. 2698 Oldfield, 0 Emsley, 2698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 285 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 57 ARG cc_start: 0.8766 (OUTLIER) cc_final: 0.7460 (ptm-80) REVERT: L 79 PHE cc_start: 0.8432 (m-80) cc_final: 0.8004 (m-80) REVERT: L 215 ASN cc_start: 0.8483 (m-40) cc_final: 0.8163 (m-40) REVERT: L 225 SER cc_start: 0.7703 (p) cc_final: 0.7313 (m) REVERT: M 80 ASP cc_start: 0.8172 (m-30) cc_final: 0.7872 (m-30) REVERT: H 126 ARG cc_start: 0.8033 (ptm-80) cc_final: 0.7540 (ptt180) REVERT: E 1 MET cc_start: 0.7447 (ttm) cc_final: 0.7169 (mtp) REVERT: F 27 GLN cc_start: 0.8332 (OUTLIER) cc_final: 0.8069 (mt0) REVERT: U 27 GLN cc_start: 0.8270 (mt0) cc_final: 0.8002 (mt0) REVERT: V 15 ARG cc_start: 0.8155 (OUTLIER) cc_final: 0.7093 (ttp-110) REVERT: c 15 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.6589 (tm-30) REVERT: f 11 MET cc_start: 0.8436 (OUTLIER) cc_final: 0.8067 (ttm) REVERT: i 19 LYS cc_start: 0.8133 (tttt) cc_final: 0.7887 (tttm) outliers start: 34 outliers final: 14 residues processed: 301 average time/residue: 0.6378 time to fit residues: 220.6077 Evaluate side-chains 292 residues out of total 2194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 273 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 57 ARG Chi-restraints excluded: chain C residue 264 PHE Chi-restraints excluded: chain L residue 259 LYS Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 307 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 239 ASP Chi-restraints excluded: chain F residue 27 GLN Chi-restraints excluded: chain I residue 27 GLN Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain P residue 35 LEU Chi-restraints excluded: chain V residue 15 ARG Chi-restraints excluded: chain W residue 13 LEU Chi-restraints excluded: chain X residue 11 MET Chi-restraints excluded: chain b residue 16 SER Chi-restraints excluded: chain c residue 15 GLU Chi-restraints excluded: chain f residue 11 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 64 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 184 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 48 optimal weight: 0.3980 chunk 10 optimal weight: 2.9990 chunk 136 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 22 optimal weight: 6.9990 chunk 212 optimal weight: 0.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 168 HIS H 90 ASN W 27 GLN i 27 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.115293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.099089 restraints weight = 31633.822| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 1.00 r_work: 0.2976 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.378 28150 Z= 0.191 Angle : 0.782 13.057 38824 Z= 0.303 Chirality : 0.039 0.144 3780 Planarity : 0.005 0.058 4704 Dihedral : 18.859 179.881 5265 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.82 % Allowed : 9.48 % Favored : 88.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.98 (0.15), residues: 2698 helix: 2.30 (0.12), residues: 1495 sheet: 0.63 (1.10), residues: 26 loop : 0.08 (0.18), residues: 1177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 13 TYR 0.026 0.002 TYR M 194 PHE 0.029 0.002 PHE L 218 TRP 0.014 0.001 TRP L 265 HIS 0.008 0.001 HIS M 183 Details of bonding type rmsd covalent geometry : bond 0.00466 (28087) covalent geometry : angle 0.78219 (38824) hydrogen bonds : bond 0.04447 ( 1317) hydrogen bonds : angle 3.93015 ( 3735) Misc. bond : bond 0.12290 ( 63) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5396 Ramachandran restraints generated. 2698 Oldfield, 0 Emsley, 2698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5396 Ramachandran restraints generated. 2698 Oldfield, 0 Emsley, 2698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 279 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 57 ARG cc_start: 0.8838 (OUTLIER) cc_final: 0.7554 (ptm-80) REVERT: L 79 PHE cc_start: 0.8458 (m-80) cc_final: 0.8008 (m-80) REVERT: M 80 ASP cc_start: 0.8152 (m-30) cc_final: 0.7852 (m-30) REVERT: H 126 ARG cc_start: 0.8092 (ptm-80) cc_final: 0.7575 (ptt180) REVERT: E 1 MET cc_start: 0.7582 (ttm) cc_final: 0.7149 (mtp) REVERT: K 14 THR cc_start: 0.8041 (OUTLIER) cc_final: 0.7821 (p) REVERT: P 11 MET cc_start: 0.8264 (ttm) cc_final: 0.7981 (ttm) REVERT: S 45 MET cc_start: 0.8804 (mtm) cc_final: 0.8590 (mtm) REVERT: V 15 ARG cc_start: 0.8283 (OUTLIER) cc_final: 0.7219 (ttp-110) REVERT: b 7 LYS cc_start: 0.8958 (OUTLIER) cc_final: 0.8465 (mtpm) REVERT: c 15 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.6676 (tm-30) REVERT: f 11 MET cc_start: 0.8518 (ttp) cc_final: 0.8142 (ttm) REVERT: i 19 LYS cc_start: 0.8219 (tttt) cc_final: 0.7980 (tttp) outliers start: 40 outliers final: 22 residues processed: 301 average time/residue: 0.6264 time to fit residues: 217.1318 Evaluate side-chains 302 residues out of total 2194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 275 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 57 ARG Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 264 PHE Chi-restraints excluded: chain L residue 259 LYS Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 217 PHE Chi-restraints excluded: chain M residue 307 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 239 ASP Chi-restraints excluded: chain A residue 11 MET Chi-restraints excluded: chain I residue 27 GLN Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain K residue 14 THR Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain N residue 52 THR Chi-restraints excluded: chain P residue 35 LEU Chi-restraints excluded: chain P residue 52 THR Chi-restraints excluded: chain Q residue 57 VAL Chi-restraints excluded: chain V residue 15 ARG Chi-restraints excluded: chain W residue 13 LEU Chi-restraints excluded: chain X residue 11 MET Chi-restraints excluded: chain b residue 7 LYS Chi-restraints excluded: chain b residue 16 SER Chi-restraints excluded: chain c residue 15 GLU Chi-restraints excluded: chain d residue 4 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 53.2217 > 50: distance: 12 - 29: 4.658 distance: 16 - 34: 5.677 distance: 20 - 42: 7.234 distance: 25 - 47: 7.826 distance: 29 - 30: 3.549 distance: 30 - 33: 5.747 distance: 31 - 32: 10.040 distance: 31 - 34: 3.792 distance: 32 - 52: 12.974 distance: 35 - 36: 3.079 distance: 37 - 63: 10.664 distance: 38 - 39: 6.674 distance: 39 - 40: 6.173 distance: 39 - 41: 7.221 distance: 42 - 43: 4.234 distance: 43 - 46: 6.561 distance: 44 - 45: 4.190 distance: 45 - 71: 24.279 distance: 47 - 48: 6.582 distance: 48 - 49: 3.504 distance: 48 - 51: 6.091 distance: 49 - 50: 5.966 distance: 50 - 78: 20.392 distance: 52 - 53: 3.855 distance: 53 - 54: 5.717 distance: 53 - 56: 3.475 distance: 54 - 55: 6.649 distance: 54 - 63: 4.796 distance: 55 - 85: 13.408 distance: 57 - 58: 3.339 distance: 57 - 59: 3.272 distance: 58 - 60: 3.157 distance: 59 - 61: 3.497 distance: 60 - 62: 4.600 distance: 61 - 62: 3.583 distance: 63 - 64: 7.433 distance: 64 - 65: 3.357 distance: 64 - 67: 5.745 distance: 65 - 66: 16.184 distance: 65 - 71: 24.327 distance: 66 - 93: 18.010 distance: 67 - 68: 4.748 distance: 68 - 69: 7.278 distance: 68 - 70: 10.333 distance: 71 - 72: 30.649 distance: 72 - 73: 12.570 distance: 72 - 75: 19.754 distance: 73 - 74: 10.638 distance: 73 - 78: 10.549 distance: 74 - 98: 15.813 distance: 75 - 76: 12.813 distance: 75 - 77: 9.198 distance: 78 - 79: 9.591 distance: 79 - 82: 5.125 distance: 80 - 81: 6.043 distance: 80 - 85: 3.049 distance: 81 - 106: 7.936 distance: 82 - 83: 5.829 distance: 82 - 84: 4.342 distance: 86 - 87: 3.589 distance: 86 - 89: 4.765 distance: 88 - 113: 6.999 distance: 89 - 90: 8.210 distance: 90 - 91: 7.650 distance: 90 - 92: 7.607 distance: 93 - 94: 5.027 distance: 94 - 95: 4.117 distance: 94 - 97: 3.818 distance: 95 - 96: 3.326 distance: 96 - 119: 4.811